I actually have three particular games I cannot not mention in this thread. While, I do have two that are more tied for first and one that barely trails behind by like a one-hundredth of a point, I have to give all three a vote.
These three games are Ocarina of Time, Majora's Mask and Wind Waker. All different in their own unique way, but all amazing games for those reasons. Now, when it comes down to which one I like best, it comes down to Majora's Mask and Ocarina of Time. I have to admit, I probably actually like Majora's Mask more. However, with Ocarina of Time being the first Zelda game I played, and the fact that I've beaten it so many times, it has a special place to me, which pretty much gives it that first place tie with Majora's Mask.
As much as I loved Wind Waker, it doesn't quite reach the levels of Majora's Mask, but is pretty close to Ocarina of Time, for me. What I liked about Wind Waker is it's more wide world feel. There were some interesting islands and even more interesting NPCs, along with my favorite soundtrack in Zelda history. It was a fun game all in all, and the bosses were actually kind of challenging. More challenging than any other Zelda game I've played, aside from maybe Majora's Mask. I also really like Medli, she has a special place to me as a character. In fact, Wind Waker and Majora's Mask, I believe, had the most amazing NPCs in the series. Medli, Makar, King of Red Lions, Tetra/Zelda and many of the other characters. It also had a bit of a humorous cartoony feel, which I loved, just because of how unique it was. Considering that Zoras couldn't really be in, I liked the race they evolved into. I loved the Ritos, and much like their Zora ancestors, they have a good taste in music. The Dragon Roost Island song is my favorite Zelda music piece ever. I also think it was better that they didn't put in Zoras. Imagine how much memory it would have took to have to do anything underwater in Wind Waker. It allowed them to expand the game. It did have some things where I would have liked to have seen more though. The sea, was kind of too vast until you found out you could get the Ballad of Gales, and you're going around in this small little boat that doesn't cover the distance as well. I felt the pace at the point was a bit slow. I would have liked a little more RPG-like elements in it. I think Wind Waker would have been perfect for RPG things. Such as enhancing your ship with items to make it faster or stronger. All in all, it was a fun game, and the NPCs were interesting.
Ocarina of Time, most everyone has it somewhere near the top of their list, and that's no exception for me. What I like about Ocarina of Time is how broad it is. It is good for a variety of players. It was easy when you knew what to do, but there's always some little puzzle that gets your mind going. It was easy enough to remember and fun enough to play though, that it made me much more eager to play it multiple times. It is, for me, the perfect Zelda game when it comes to replay ability. Many of the songs are classic, as is the time travel. Maybe not as amazing of a soundtrack as Wind Waker, but still good nonetheless. Fun puzzles, well-thought out bosses and dungeons, a great final battle, with a good story, that's what I like about it. It's just something I can pick up no matter what kind of mood I'm in, and play it. Which is unlike pretty much any other game I've ever played. It also is special for being the first Zelda game I played. As I admitted earlier though, I don't find it any better than Majora's Mask or even really Wind Waker.
Then there's Majora's Mask. I found the difficulty of this game similar to Wind Waker, at least for the bosses. The bosses started off pretty tough, and got easier as the game progressed. Aside from Gyorg and the first form of Majora's Mask. This may sound weird and all, but I also really loved the Goron Maze on the Moon. It took me forever to get that Piece of Heart, but just going down that track was fun for me. This is also the only Zelda game for me, where I feel the NPCs are as good as, or better than those in Wind Waker. The place where Majora's Mask excels in that part, is that all the characters have some sort of story relevance to the plot. Whereas Wind Waker's were a bit more, just there, as fun as they were, just there. Majora's Mask gave the NPCs a real role, gave the characters their own development, and provided some fun quests. No matter how awkward the quest was. I'm looking at you Mystery Hand! The story was unique and compelling as well. It was like Wind Waker, without the minor cons of gameplay. I also loved all the things the masks did. It was really just an amazing game.
My Current Ratings for these three games:
Majora's Mask: 9.8
Ocarina of Time: 9.8
Wind Waker: 9.79
OoT would probably have the same rating as Wind Waker without the classic feel. It revolutionized 3D Zelda.
From what I've seen of Skyward Sword, these games may have some stiff competition soon.